LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -46.293629 0.0000000) to (32.734539 46.293629 5.1122761) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5888237 6.2101209 5.1122761 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -46.293629 0.0000000) to (32.734539 46.293629 5.1122761) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5888237 6.2101209 5.1122761 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -46.293629 0.0000000) to (32.734539 46.293629 5.1122761) create_atoms CPU = 0.004 seconds 660 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_469343973171_005#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.082 | 5.082 | 5.082 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4195.741 0 -4195.741 91183.811 141 0 -4632.1659 0 -4632.1659 4160.6711 Loop time of 5.37892 on 1 procs for 141 steps with 1312 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4195.74097649496 -4632.16226928966 -4632.16585017891 Force two-norm initial, final = 861.70389 0.17378603 Force max component initial, final = 158.82757 0.011553064 Final line search alpha, max atom move = 1.0000000 0.011553064 Iterations, force evaluations = 141 270 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2333 | 5.2333 | 5.2333 | 0.0 | 97.29 Neigh | 0.055066 | 0.055066 | 0.055066 | 0.0 | 1.02 Comm | 0.048117 | 0.048117 | 0.048117 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04239 | | | 0.79 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7306.00 ave 7306 max 7306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188456.0 ave 188456 max 188456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188456 Ave neighs/atom = 143.64024 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 141 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.077 | 5.077 | 5.077 Mbytes Step Temp E_pair E_mol TotEng Press Volume 141 0 -4632.1659 0 -4632.1659 4160.6711 15494.292 147 0 -4632.3796 0 -4632.3796 -100.50862 15541.473 Loop time of 0.177488 on 1 procs for 6 steps with 1312 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4632.16585017887 -4632.37939211232 -4632.37962542568 Force two-norm initial, final = 95.027758 2.0345294 Force max component initial, final = 92.513729 1.4456853 Final line search alpha, max atom move = 0.00034001831 0.00049155946 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17121 | 0.17121 | 0.17121 | 0.0 | 96.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014272 | 0.0014272 | 0.0014272 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00485 | | | 2.73 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7084.00 ave 7084 max 7084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186976.0 ave 186976 max 186976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186976 Ave neighs/atom = 142.51220 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.3796 0 -4632.3796 -100.50862 Loop time of 6.345e-06 on 1 procs for 0 steps with 1312 atoms 189.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.345e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7092.00 ave 7092 max 7092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186456.0 ave 186456 max 186456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186456 Ave neighs/atom = 142.11585 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.215 | 5.215 | 5.215 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -4632.3796 -4632.3796 32.675372 93.034685 5.1124227 -100.50862 -100.50862 -148.76688 -145.48559 -7.2733901 2.3586279 615.77972 Loop time of 6.756e-06 on 1 procs for 0 steps with 1312 atoms 281.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.756e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7092.00 ave 7092 max 7092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93228.0 ave 93228 max 93228 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186456.0 ave 186456 max 186456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186456 Ave neighs/atom = 142.11585 Neighbor list builds = 0 Dangerous builds = 0 1312 -4632.38618542568 eV 2.35862786104821 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06